Contacts of the helix formed by residues 194 - 202 (chain L) in PDB entry 1VCB
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 194 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85L LEU* 6.1 1.1 - - + -
87L VAL* 5.0 6.1 - - + -
95L PRO* 4.5 16.6 - - + -
118L LEU* 4.0 33.0 - - + -
120L ARG* 4.0 27.8 - - + +
125L HIS* 4.4 19.5 - - + -
193L ASN* 1.3 71.2 + - - +
195L GLN* 1.3 60.6 + - - +
197L ASP* 3.3 7.6 + - - +
198L LEU* 2.9 37.3 + - + +
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Residues in contact with GLN 195 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93L GLY 5.2 3.8 + - - -
94L GLU* 4.1 13.8 + - - +
95L PRO* 3.7 24.8 - - + +
193L ASN* 3.2 8.5 + - - +
194L VAL* 1.3 75.4 - - - +
196L LYS* 1.3 61.3 + - - +
198L LEU* 3.2 20.8 + - - +
199L GLU* 2.9 54.8 + - - +
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Residues in contact with LYS 196 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190L ASP* 5.7 5.2 - - - +
193L ASN* 2.9 31.7 + - + +
194L VAL 3.2 0.2 - - - -
195L GLN* 1.3 78.8 - - - +
197L ASP* 1.3 58.1 + - - +
199L GLU* 3.2 24.5 + - - +
200L ARG* 2.9 73.3 + - + +
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Residues in contact with ASP 197 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118L LEU* 6.1 1.6 - - + -
120L ARG* 2.9 32.1 + - - +
125L HIS 5.4 1.4 - - - +
127L GLY* 5.4 2.3 + - - -
192L PRO* 5.6 2.3 - - - +
193L ASN 3.0 25.3 + - - +
194L VAL 3.7 4.7 - - - +
196L LYS* 1.3 76.3 - - - +
198L LEU* 1.3 61.0 + - + +
200L ARG* 3.3 12.1 + - - +
201L LEU* 2.9 38.1 + - + +
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Residues in contact with LEU 198 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 3.7 24.9 - - + +
89L LEU* 3.8 27.6 - - + -
93L GLY 4.4 6.7 - - - +
95L PRO* 3.6 31.2 - - + -
118L LEU* 3.9 17.3 - - + -
135L LEU* 5.2 0.4 - - + -
194L VAL* 2.9 22.3 + - + +
195L GLN* 3.5 20.0 - - - +
197L ASP* 1.3 75.6 - - - +
199L GLU* 1.3 56.6 + - - +
201L LEU* 3.2 9.8 + - + +
202L THR* 2.7 39.8 + - - +
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Residues in contact with GLU 199 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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195L GLN* 2.9 45.2 + - - +
196L LYS* 3.5 32.0 + - - +
198L LEU* 1.3 76.4 - - - +
200L ARG* 1.3 64.9 + - - +
202L THR* 3.7 6.7 - - - -
203L GLN* 2.9 30.3 + - - +
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Residues in contact with ARG 200 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196L LYS* 2.9 79.3 + - + +
197L ASP* 3.3 15.3 - - - +
198L LEU 3.0 0.2 - - - -
199L GLU* 1.3 82.1 + - - +
201L LEU* 1.3 68.8 + - + +
203L GLN* 3.0 26.6 + - - +
204L GLU* 3.6 4.0 + - - +
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Residues in contact with LEU 201 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 4.1 11.2 - - + -
118L LEU* 5.4 2.7 - - + -
134L GLU* 4.1 32.5 - - + +
135L LEU* 4.1 35.4 - - + -
197L ASP* 2.9 26.4 + - + +
198L LEU* 3.8 15.7 - - + +
200L ARG* 1.3 72.7 - - + +
202L THR* 1.3 63.5 + - - +
204L GLU* 3.0 26.3 + - + +
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Residues in contact with THR 202 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63L LEU* 3.6 27.2 - - + +
198L LEU* 2.7 23.6 + - - +
199L GLU* 3.7 7.7 - - - -
201L LEU* 1.3 72.9 - - - +
203L GLN* 1.3 52.7 + - - +
204L GLU* 2.6 22.7 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il